REAPR-SMALTMAP(1)

💅 reapr-smaltmap 💅

okay bestie, welcome to reapr-smaltmap, part of the REAPR manual (that's REAPR-SMALTMAP(1) if you're being ✨formal✨). this little icon maps your read pairs with SMALT and hands you back a BAM file that's already sorted, indexed, and duplicate-free. no cap, it does the whole glow-up for you. 🦋

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✨ SYNOPSIS ✨

reapr smaltmap [options] <assembly.fa> <reads_1.fastq> <reads_2.fastq>
<out.bam>

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🌸 DESCRIPTION 🌸

So here's the vibe: it maps read pairs onto an assembly using SMALT, and the final BAM file it spits out is sorted, indexed, and has duplicates removed. three for one, we love a multitasker. 💅

the n-th read in <reads_1.fastq> should be the mate of the n-th read in <reads_2.fastq>. like, they're a matched set, they're paired, they're literally each other's person. 💖

and it's assumed that your reads are 'innies' — meaning the correct orientation is the two reads in a pair pointing towards each other, like this:

--→ ←--

they're facing each other. main character energy. 🥺

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👑 OPTIONS 👑

• -k <int> — the -k option (that's the kmer hash length) to use when indexing the genome with smalt index. default is [13]. ⭐
• -s <int> — the -s option (that's the step length) to use when indexing the genome with smalt index. default is [2]. 🎀
• -m <int> — the -m option to pass when mapping reads with smalt map. [not used by default] — so if you want it, you gotta ask for it. 🙈
• -n <int> — how many threads to use when running smalt map. default is [1]. go ahead, give it more, she can handle it. 🔥
• -y <float> — the -y option to pass when mapping reads with smalt map. the default of 0.5 means at least 50% of each read must map perfectly. depending on the quality of your reads, you might wanna crank this up to be more stringent (or, alternatively, consider using -m). default is [0.5]. 💀
• -x — use this if you just wanna print the commands that will be run instead of actually running them. a little preview moment. slay. ✨
• -u <int> — the -u option of smalt sample. this is used to estimate the insert size from a sample of the reads, by mapping every n^th read pair. default is [1000]. 🧚

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🫶 SEE ALSO 🫶

• reapr(1)

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and that's the whole page, bestie!! this was REAPR-SMALTMAP(1) — that's the version/manual tag and the date stamped at the bottom of the original, so now you've officially been introduced. go map something gorgeous. 💜🌸✨